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One could argue that an additional energy-intensive process, fat synthesis, or an increase in this process, would, for the same amount of excess energy intake, result in decreased fat deposition due to the higher energy costs in maintaining the synthesis.

Hast hit it, friend wiggle.

Next couple o'questions...

2) How well quantified are the various metabolic energy pathways? Can the body "deliberately" change to more or less efficient was of burning up your food depending on the amount of white / brown fat and your diet? Can one reset these markers over the short or long term by tweaking the *composition* of the diet rather than total calories?

Cheers!

1) Is it possible that the body keeps track of its amount of brown vs. white fat, exercise levels, and both TOTAL caloric intake and % of protein / carbs / fat, and then decides how much food to absorb, or to process for energy once absorbed, instead of excreting it unused? I.e. is the number of calories your body "sees" when deciding to become overweight, necessarily the number of kcal which would be released by oxidizing the food in a bomb calorimeter?

The amount of brown fat in adults is very small. It serves a purpose in infants and small mammals by allowing a futile cycle in which heat versus ATP (etc.) is generated in order to keep the small body warm. It does this by uncoupling the mitochondrial electron chain from oxidative phosphorylation. The reason the fat is brown is because of a high number of mitochondria. The body does count calories and there is a lot of spontaneous adjustment between intake and expenditure in younger adults. The older you get, the less robust this coordination. In one study younger men who were either overfed or underfed for a relatively long period of time spontaneously adjusted their intake to gain or to lose weight to get back to their original long term weight. Elderly men either stayed underweight or overweight after the period of under or overfeeding. Once you ingest something, you're stuck with over 98% of its nutritive value unless you increase your energy expenditure or decrease your subsequent food intake. You can't excrete absorbed macronutrients you "don't need."

2) How well quantified are the various metabolic energy pathways? Can the body "deliberately" change to more or less efficient was of burning up your food depending on the amount of white / brown fat and your diet? Can one reset these markers over the short or long term by tweaking the *composition* of the diet rather than total calories?

The different metabolic pathways are about as well characterized as anything in science. As I said before, outside of mice, voles, shrews, and infants, there isn't a whole lot of brown fat activity going on. It may be that those folks who can eat anything without gaining weight have a higher percentage of brown fat. But it would be a really, really bad thing to be able to increase people's quantity of brown fat. It sounds good, but what it really means is that it would take a much larger food budget to do exactly the same thing. The rest of the food is getting burned up in a futile cycle to produce heat. Increase everyone's energy expenditure by 20% and you've essentially increased the world's population by 20 percent. Can the world's farms take such a hit? The point of shifting substrate oxidation appears to be an automatic way the body has of dealing with greater or lesser relative amounts of macronutrients in such a way as to protect the body's health. Sure, increasing obesity may be a bad thing, but it's not as bad over the same length of time as glycosylated proteins from too high a blood serum glucose level.